Investigation Title	Transcription profiling of Arabidopsis wild type and hfr1/sics1 knock-out mutant seedlings exposed to low R/FR light
Comment[Submitted Name]	Ruberti - A.thaliana Shade Avoidance Response wt and hfr1-sics1
Experimental Design	genetic_modification_design	transcription profiling by array
Experimental Design Term Source REF	mo	EFO
Comment[ArrayExpressReleaseDate]	2006-03-01
Comment[AEMIAMESCORE]	5
Comment[ArrayExpressAccession]	E-MEXP-444
Comment[MAGETAB TimeStamp_Version]	2011-06-28 21:02:39 Last Changed Rev: 14857
Experimental Factor Name	time	light
Experimental Factor Type	time	light
Experimental Factor Term Source REF
Person Last Name	Sessa	Ciolfi	Possenti	Becker	Ruberti	Carabelli	Morelli	Mittempergher	Sassi
Person First Name	Giovanna	Andrea	Marco	Jorg	Ida	Monica	Giorgio	Francesca	Massimiliano
Person Mid Initials
Person Email					ida.ruberti@uniroma1.it
Person Phone					+390649912211
Person Fax					+390649912500
Person Address					P.le Aldo Moro 5
Person Affiliation	CNR	CNR	INRAN	IGC	Institute of Molecular Biology and Pathology	CNR	INRAN	CNR	CNR
Person Roles					submitter
Person Roles Term Source REF
Quality Control Type
Quality Control Term Source REF
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date	2006-03-01
PubMed ID	23893169
Publication DOI	16322556
Publication Author List	Andrea Ciolfi; Giovanna Sessa; Massimiliano Sassi; Marco Possenti; Samanta Salvucci; Monica Carabelli; Giorgio Morelli; Ida Ruberti
Publication Title	Dynamics of the Shade-Avoidance Response in Arabidopsis
Publication Status	journal_article
Publication Status Term Source REF
Experiment Description	Aim of the experiment is the identification of genes differentially regulated in hfr1/sics1 seedlings relative to wild type after prolonged exposure to low R/FR. To this end, gene expression changes were analysed in Arabidopsis wild-type and hfr1/sics1 knock-out mutant seedlings exposed to low R/FR light. The experiment was designed to enable comparison between the different genotypes exposed or not exposed to low R/FR light.
Protocol Name	P-MEXP-9651	P-MEXP-9609	P-MEXP-9615	P-MEXP-9618	Affymetrix:Protocol:Hybridization-EukGE-WS2v4	P-AFFY-6	Affymetrix:Protocol:ExpressionStat
Protocol Type	specified_biomaterial_action	grow	nucleic_acid_extraction	labeling	hybridization	feature_extraction	bioassay_data_transformation
Protocol Description	Arabidopsis seedlings were exposed to high R/FR light and then to low R/FR light for a period of time. Light outputs in high R/FR were: 670 nm (Red) 96 mmoles m-2s-1; 735 nm (Far Red) 21 mmoles m-2s-1; 470 nm (Blue) 15 mmoles m-2s-1. Light outputs in low R/FR were: 670 nm, 12 mmoles m-2s-1; 735 nm, 105 mmoles m-2s-1; 470 nm, 15 mmoles m-2s-1. 7-day-old wild-type and hfr1/sics1 (hfr1-4/sics1-1 and hfr1-5/sics1-2) seedlings were either maintained in high R/FR or transferred to low R/FR for 1 day, and then harvested.	Seedlings were grown in a growth chamber (E30-LED, Percival Scientific Inc., USA), at 21°C temperature, 75% humidity, 16 h light/8 h dark cycles.	Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Germany). Each sample consists of a pool of 200 individuals. Two sets of samples were collected from independent experiments.	7 µg of total RNA was used in a reverse transcription reaction (SuperScript II; Invitrogen, Paisley, UK) to generate first-strand cDNA. After second-strand synthesis, double-strand cDNA was used in an in vitro transcription (IVT) reaction to generate biotinylated cRNA (ENZO BioArray HighYield RNA Transcript Labeling Kit; ENZO Diagnostics, Farmingdale, NY). Size distribution of the cRNA and fragmented cRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.	Title: Fluidics Station Protocol. Description: 	Title: Affymetrix CEL analysis. Description: 	Title: Affymetrix CHP Analysis (ExpressionStat). Description:
Protocol Parameters		start time;min temperature;	Amplification;Extracted product;	Amplification;Label used;Amount of nucleic acid labeled;
Protocol Hardware
Protocol Software					MicroArraySuite 5.0	MicroArraySuite 5.0	MicroArraySuite 5.0
Protocol Contact
Protocol Term Source REF	mo
SDRF File	E-MEXP-444.sdrf.txt
Term Source Name	mo		ncbitax	tair_dev:1.27	The MGED Ontology	tair	ArrayExpress	mo	EFO
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php		http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	http://www.arabidopsis.org/info/ontologies/	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://arabidopsis.org	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/
Term Source Version				1.27